Cloning and characterization of interferon stimulated genes Viperin and ISG15, and their promoters from snakehead Channa argus

By suppression subtractive hybridization, rapid amplification of cDNA ends and gene walking methods, interferon stimulated genes (ISGs), Viperin and ISG15, and their promoters have been cloned and characterized from snakehead Channa argus. The Viperin cDNA was found to be 1474 nt and contain an open reading frame (ORF) of 1059 nt that translates into a putative peptide of 352 amino acid (aa). The putative peptide of Viperin shows high identity to that in teleosts and mammals except for the N-terminal 70 aa. The ISG15 cDNA was found to be 758 nt and contain an ORF of 468 nt that translates into a putative peptide of 155 aa. The putative peptide of ISG15 is composed of two tandem repeats of ubiquitin-like (UBL) domains, and a canonical conjugation motif (LRGG) at C-terminal. Viperin and ISG15 promoter regions were characterized by the presence of interferon stimulating response elements (ISRE) and gamma-IFN activation sites (GAS). ISRE is a feature of IFN-induced gene promoter and partially overlaps interferon regulatory factor (IRF) 1 and IRF2 recognition sites. GAS is responsible for the gamma-IFN mediated transcription. One conserved site for NF-kappa B was found in the promoter region of Viperin. This is the first report of conservative binding motif for NF-kappa B in accordance with the consensus sequence (GGGRN-NYYCC) among teleost ISG promoters. Moreover, there were also TATA, CAAT and Sp1 transcription factor sites in Viperin and ISG15 promoters. In 5' untranslated region (UTR), snakehead ISG15 gene contains a single intron, which differs from Viperin gene. The transcripts of Vipeirn and ISG15 mRNA were mainly expressed in head kidney, posterior kidney, spleen and gill. The expression levels in liver were found to increase obviously in response to induction by IFN-inducer poly I : C.

REEVALUATION OF 2,2-BIPYRIDINE AND PYRAZINE AS PROMOTERS FOR DIRECT ELECTRON-TRANSFER BETWEEN CYTOCHROME-C AND METAL-ELECTRODES

Results from previous electrochemical studies have indicated that 2,2'-bipyridine and pyrazine do not function as promoters for heterogeneous electron transfer between cytochrome c and metal electrodes. Their lack of activity was attributed to the improper positioning of the two functional groups in 2,2'-bipyridine and the inefficient length of pyrazine. In the present study it was determined that both 2,2'-bipyridine and pyrazine act as promoters when self-absorbed over a sufficiently long dipping time or at roughened electrodes. The promoter characteristics of these two molecules were studied and compared with those of 4,4'-bipyridine. The difference in their promoter behavior appears to result primarily from their different strengths of adsorption and not because electrodes modified with 2,2'-bipyridine or pyrazine are unsuitable for accelerating direct electron transfer reactions in cytochrome c. These results have implications regarding the mechanism(s) of promoter effects in electrochemical reactions of cytochrome c.

Single base-resolution methylome of the silkworm reveals a sparse epigenomic map

Epigenetic regulation in insects may have effects on diverse biological processes. Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). We conservatively estimate that 0.11% of genomic cytosines are methylcytosines, all of which probably occur in CG dinucleotides. CG methylation is substantially enriched in gene bodies and is positively correlated with gene expression levels, suggesting it has a positive role in gene transcription. We find that transposable elements, promoters and ribosomal DNAs are hypomethylated, but in contrast, genomic loci matching small RNAs in gene bodies are densely methylated. This work contributes to our understanding of epigenetics in insects, and in contrast to previous studies of the highly methylated genomes of Arabidopsis(1) and human(2), demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation.

A possible mode of the specific recognition of nucleic acids by proteins

Seven sets of protein target sites, which occur in several gene promoters, have been analyzed. The results suggest that there is a possible mode of specific recognition of double-helical nucleic acids by proteins, This recognition mode is related to a spe

Expression pattern, cellular localization and promoter activity analysis of ovarian aromatase (Cyp19a1a) in protogynous hermaphrodite red-spotted grouper

Aromatase plays a key role in sex differentiation of gonads. In this study, we cloned the full-length cDNA of ovarian aromatase from protogynous hermaphrodite red-spotted grouper (Epinephelus akaara), and prepared the corresponding anti-EaCyp19a1a antiserum. Western blot and immunofluorescence studies revealed ovary-specific expression pattern of EaCyp19a1a in adults and its dynamic expression change during artificial sex reversal. EaCyp19a1a was expressed by follicular cells of follicular layer around oocytes because strong EaCyp19a1a immunofluorescence was observed in the cells of ovaries. During artificial sex reversal, EaCyp19a1a expression dropped significantly from female to male, and almost no any positive EaCyp19a1a signal was observed in testicular tissues. Then, we cloned and sequenced a total of 1967 bp T-flanking sequence of EaCyp19a1a promoter, and showed a number of potential binding sites for some transcriptional factors, such as SOX5, GATA gene family, CREB, AP1, FOXL1, C/EBP, ARE and SF-1. Moreover, we prepared a series of 5' deletion promoter constructs and performed in vitro luciferase assays of EaCyp19a1a promoter activities. The data indicated that the CREB regulation region from -1010 to -898 might be a major cis-acting element to EaCyp19a1a promoter, whereas the elements GATA and SOX5 in the region from -1216 to -1010 might be suppression elements. Significantly, we found a common conserved sequence region in the fish ovary-type aromatase promoters with identities from 93% to 34%. And, the motifs of TATA box, SF-1, SOX5, and CREB existed in the region and were conserved among the most of fish species. (C) 2009 Elsevier Ireland Ltd. All rights reserved.

Hybrid cytomegalovirus-U6 promoter-based plasmid vectors improve efficiency of RNA interference in zebrafish

Short hairpin RNA (shRNA) directed by RNA polymerase III (Pol III) or Pol II promoter was shown to be capable of silencing gene expression, which should permit analyses of gene functions or as a potential therapeutic tool. However, the inhibitory effect of shRNA remains problematic in fish. We demonstrated that silencing efficiency by shRNA produced from the hybrid construct composed of the CMV enhancer or entire CMV promoter placed immediately upstream of a U6 promoter. When tested the exogenous gene, silencing of an enhanced green fluorescent protein (EGFP) target gene was 89.18 +/- 5.06% for CMVE-U6 promoter group and 88.26 +/- 6.46% for CMV-U6 promoter group. To test the hybrid promoters driving shRNA efficiency against an endogenous gene, we used shRNA against no tail (NTL) gene. When vectorized in the zebrafish, the hybrid constructs strongly repressed NTL gene expression. The NTL phenotype occupied 52.09 +/- 3.06% and 51.56 +/- 3.68% for CMVE-U6 promoter and CMV-U6 promoter groups, respectively. The NTL gene expression reduced 82.17 +/- 2.96% for CMVE-U6 promoter group and 83.06 +/- 2.38% for CMV-U6 promoter group. We concluded that the CMV enhancer or entire CMV promoter locating upstream of the U6-promoter could significantly improve inhibitory effect induced by the shRNA for both exogenous and endogenous genes compared with the CMV promoter or U6 promoter alone. In contrast, the two hybrid promoter constructs had similar effects on driving shRNA.

Gene structures and promoter characteristics of interferon regulatory factor 1 (IRF-1), IRF-2 and IRF-7 from snakehead Channa argus

Three interferon regulatory factor (IRF) genes, CaIRF-1, CaIRF-2 and CaIRF-7, and their promoters of snakehead (Channa argus) were cloned and characterized. The CaIRF-1 gene consists of ten exons, spans 4.3 kb and encodes a putative peptide of 299 aa. The CaIRF-2 gene consists of nine exons, spans 8 kb and encodes a putative peptide of 328 aa. The gene organizations of CaIRF-1 and CaIRF-2 are very similar to that of human IRF-1 and IRF-2 except more compact. Comparison of exon-intron organization of the two genes indicated a common evolutionary structure, notably within the exons encoding the DNA binding domain (DBD) of the two factors. The CaIRF-7 gene spans 4.1 kb and encodes a putative peptide of 437 aa. However, the gene organization of CaIRF-7 consisting of ten exons is different to human IRF-7a gene which has an intron in 5' UTR. Three CaIRFs share homology in N-terminal encompassing the DBD that contains a characteristic repeat of tryptophan residues. The promoters of CaIRF-1 and CaIRF-2 genes contain the conserved sites for NF-kappa B and Sp1. The gamma-IFN activation sites (GAS) were found in the promoters of CaIRF-1 and CaIRF-7. The promoter of CaIRF-7 contains conserved interferon stimulating response element (ISRE) which is characteristic of IFN-induced gene promoter, and suggests that there also exist intracellular amplifier circuit in fish IFN signal pathway. Moreover, the element GAAANN oriented in both directions is repeated in CaIRF promoter regions, which confers to further inducibility by IFN. The constitutive expression of CaIRF genes were found to increase obviously in response to induction by the known IFN-inducer poly I:C. (c) 2008 Published by Elsevier Ltd.

Retention of the developmental pluripotency in medaka embryonic stem cells after gene transfer and long-term drug selection for gene targeting in fish

Embryonic stem (ES) cells provide a unique tool for introducing random or targeted genetic alterations, because it is possible that the desired, but extremely rare recombinant genotypes can be screened by drug selection. ES cell-mediated transgenesis has so far been limited to the mouse. In the fish medaka (Oryzias latipes) several ES cell lines have been made available. Here we report the optimized conditions for gene transfer and drug selection in the medaka ES cell line MES1 as a prelude for gene targeting in fish. MES1 cells gave rise to a moderate to high transfection efficiency by the calcium phosphate co-precipitation (5%), commercial reagents Fugene (11%), GeneJuice (21%) and electroporation (>30%). Transient gene transfer and CAT reporter assay revealed that several enhancers/promoters and their combinations including CMV, RSV and ST (the SV40 virus early gene enhancer linked to the thymidine kinase promoter) were suitable regulatory sequences to drive transgene expression in the MES1 cells. We show that neo, hyg or pac conferred resistance to G418, hygromycin or puromycin for positive selection, while the HSV-tk generated sensitivity to ganciclovir for negative selection. The positive-negative selection procedure that is widely used for gene targeting in mouse ES cells was found to be effective also in MES1 cells. Importantly, we demonstrate that MES1 cells after gene transfer and long-term drug selection retained the developmental pluripotency, as they were able to undergo induced differentiation in vitro and to contribute to various tissues and organs during chimeric embryogenesis.

转座子Minos介导的果蝇转基因平台构建及水稻高表达启动子的克隆 任娟 指

本实验室果蝇研究工作，主要集中在黑腹果蝇的新基因起源的研究。新基因起源的分子机制主要包括：外显子重排、基因复制、基因逆转座、移动元件介导、基因水平转移、基因从头起源、基因的断裂融合。为了阐述这些新基因的产生和它们所带来的物种适应性，我们对这些新近起源的基因进行了功能研究。但是，仅仅限于新基因所在物种的功能研究并不能完全解释新基因产生的进化原因，我们需要了解它是否能够给没有该基因的果蝇物种带来一定的适应性。例如一些生殖相关新基因，如果我们将它们转入没有该基因的果蝇，那是否能够给该果蝇带来生殖能力的提高？无论结果如何，这都为我们研究新基因的起源提供一个重要线索。由此，黑腹果蝇以外的其它果蝇物种中实现转基因成为该研究的重要技术环节。但是，实验室目前的转基因系统仅限于P转座子介导的黑腹果蝇转基因系统，因而我们需要建立一种新的转基因平台。而转座子Minos打破物种范围的转基因特性，以及它的转座特点为我们提供了选择。转座子Minos是从果蝇D. hydei中克隆出来长约1.8kb的Ⅱ型转座子，Tc1家族转座元件成员。Minos的转座机制与大部分转座子一样，在宿主基因组里面实行着剪切和粘贴的运作机制。Minos在转座时，偏向插入TA位点并且主要集中于内含子区域，这样可以减少对插入位置基因的影响。此外，Minos在黑腹果蝇中的转座效率约30%，并且拥有一套成熟的选择标记。因此，Minos成为我们解决非黑腹果蝇转基因技术难题的首选。 在本文的工作中，我们采用由希腊Savakis教授（希腊分子生物学与生物技术研究所）提供的Minos转基因系统，完成果蝇的转基因实验。在这套转基因系统中，非自主的转座子Minos和转座酶基因被克隆到了不同载体当中。其中Minos转座子序列中插入了由3xP3眼睛特异表达的启动子介导表达的eGFP报告基因，而转座酶基因则由热激蛋白hsp70启动子调控表达。实验过程中，我们在果蝇D. melanogaster 和D. yakuba的胚胎中分别同时显微注射入含有转座子和转座酶本实验室果蝇研究工作，主要集中在黑腹果蝇的新基因起源的研究。新基因起源的分子机制主要包括：外显子重排、基因复制、基因逆转座、移动元件介导、基因水平转移、基因从头起源、基因的断裂融合。为了阐述这些新基因的产生和它们所带来的物种适应性，我们对这些新近起源的基因进行了功能研究。但是，仅仅限于新基因所在物种的功能研究并不能完全解释新基因产生的进化原因，我们需要了解它是否能够给没有该基因的果蝇物种带来一定的适应性。例如一些生殖相关新基因，如果我们将它们转入没有该基因的果蝇，那是否能够给该果蝇带来生殖能力的提高？无论结果如何，这都为我们研究新基因的起源提供一个重要线索。由此，黑腹果蝇以外的其它果蝇物种中实现转基因成为该研究的重要技术环节。但是，实验室目前的转基因系统仅限于P转座子介导的黑腹果蝇转基因系统，因而我们需要建立一种新的转基因平台。而转座子Minos打破物种范围的转基因特性，以及它的转座特点为我们提供了选择。转座子Minos是从果蝇D. hydei中克隆出来长约1.8kb的Ⅱ型转座子，Tc1家族转座元件成员。Minos的转座机制与大部分转座子一样，在宿主基因组里面实行着剪切和粘贴的运作机制。Minos在转座时，偏向插入TA位点并且主要集中于内含子区域，这样可以减少对插入位置基因的影响。此外，Minos在黑腹果蝇中的转座效率约30%，并且拥有一套成熟的选择标记。因此，Minos成为我们解决非黑腹果蝇转基因技术难题的首选。 在本文的工作中，我们采用由希腊Savakis教授（希腊分子生物学与生物技术研究所）提供的Minos转基因系统，完成果蝇的转基因实验。在这套转基因系统中，非自主的转座子Minos和转座酶基因被克隆到了不同载体当中。其中Minos转座子序列中插入了由3xP3眼睛特异表达的启动子介导表达的eGFP报告基因，而转座酶基因则由热激蛋白hsp70启动子调控表达。实验过程中，我们在果蝇D. melanogaster 和D. yakuba的胚胎中分别同时显微注射入含有转座子和转座酶所在的质粒。转座酶在37度条件诱导下进行表达，协助Minos完成转座过程。在转基因果蝇的阳性筛选中，我们利用眼睛特异表达的绿色荧光蛋作为选择标记。并且，我们通过PCR实验进一步验证了转基因果蝇的真实性。本研究中，我们对转基因实验条件进行了初步优化。我们通过对黑腹果蝇白眼突变品系W1118和D. yakuba注射后胚胎进行保湿，对D. yakuba注射胚胎进行非退壳处理。在改进条件下W1118和D. yakuba的存活率分别为10%和3%左右。通过筛选转基因阳性果蝇，我们得出Minos在W1118和D. yakuba中的转座效率分别在32%和20%左右。我们的实验结果再一次证实了Minos在果蝇D. melanogaster中可行性。同时，该工作也初步完成了在果蝇D. yakuba 中的第一次Minos介导的转基因实验，为新基因的跨物种功能研究奠定了实验基础。在未来的工作计划中，我们将采用Minos转基因系统，把实验室目前研究的黑腹果蝇新基因导入其它物种果蝇进行功能研究。 水稻是一种重要的世界粮食作物，世界上过半的人口以水稻为主食。水稻相对别的粮食作物来讲具有较小的基因组，并且拥有较好的基因组注释，是一种理想的单子叶模式生物。植物转基因技术的发展推动着水稻功能基因组学的研究，目前水稻的转基因技术主要依赖于土壤细菌农杆菌（Agrobacterium tumefaciens）T-DNA介导的外源基因染色体插入。在自然状态下，农杆菌的T-DNA位于Ti致瘤质粒当中。它包括了一些转座元件和一些帮助T-DNA转座的毒性蛋白基因和调节基因。由于Ti质粒上的T-DNA太长，并且没有太多的酶切位点，因此自然状态的T-DNA不适合进行转基因实验。为了方便T-DNA的实际应用，研究人员创立了双载体转基因系统。T-DNA转座区被分离到出Ti载体，并且装载到另外一个适合实验操作的质粒当中，而毒性蛋白表达基因等则保留在Ti质粒上。因此，在进行T-DNA介导的转基因实验时，需要同时存在T-DNA载体和Ti质粒。 本文以“水稻注释计划数据库RAP-DB”的表达数据为参考，选择了60个高表达基因的启动子区域进行克隆。通过对T-DNA载体pCAMBIA1301 进行改造，去掉其原来的35S启动子，将预测的基因启动子克隆到该载体中并与报告基 摘要 因GUS 基因融合。通过分子克隆实验，我们得到了45个高表达基因的启动子载体。最终，为了测试这45个启动子的启动效率，我们会将它们转化到水稻愈伤组织中通过启动子融合的GUS基于表达情况来判断我们启动子的启动效率。